The population structure of two pathogenic fungi, Histoplasma capuslatum which reproduces both sexually and asexually and Coccidioides immitis which reproduces only asexually, will be analyzed by nucleic acid variation. These population genetic data will insure the ability of PCR-mediated detection protocols to identify variable strains and isolates, and will address the recently posed, fundamental paradox that sexual fungi have a clonal population structure in nature, while some asexual fungi seem to be recombining. The PCR-mediated detection protocol will be clinically important by detecting disease rapidly, especially in immunodeficient patients. Discriminating between clonal or recombining fungal populations will be important to recognizing virulent strains or pathogenicity genes, and to understanding fungal resistance to drug therapy. The proposed study follows the lead of bacterial population biologists, and will complement ongoing studies, elsewhere, of the population biology of ascomycete pathogenic yeasts. Genomic variation will be determined at many polymorphic loci by hybridization between genomic DNA from many isolates and cloned or PCR amplified probes, or by denaturing gradient gel electrophoresis of PCR amplified regions. The presence or absence of recombination will be determined by pairwise comparison of multilocus genotypes as has been done for isozyme data, and by the new parsimony methods which borrow from phylogenetic analysis. Isolates will come from two clinical collections for each fungus, and the study will be extended to environmental isolates and international isolates. This study follows on the phylogenetic analysis of many important ascomycete fungal pathogens and their nonpathogenic relatives and both the proposed and previous studies are broadly applicable to plant pathology and food microbiology, as well as medical mycology.